Brandon, looks like you've cleaned up the area pretty well. I have to agree with what Phil had to say. Also, Hydro Junkie mentioned West Systems silica fibers (406). I think that would work better than micro balloons. I'm doing some work at the present with epoxy and micro balloons. The work I'm doing doesn't require much strength. Learned that too much micro balloons makes for a week spot compared to straight epoxy. Doesn't cure as hard as fast as epoxy alone. Haven't used the 406 silica fibers. But I do have it on hand in case I need it. Can't tell for sure but, it looks like the plywood you have in the one photograph is three ply. If it's possible I myself would rather have more ply than that. As long as the holes aren't badly oil soaked... Straight epoxy should do just fine. The back of these hulls are pretty strong and solid. As long as any hardware is mounted on a good flat surface it should be fine.
Got one last thing to say... Brandon, welcome to my favorite class Sport 40!!! Ken Wheeler